[maker-devel] Patch for a bug with repeat gff

[Anthony Bretaudeau]

Hi,
Here is a minimal gff file that allows to reproduce the bug. It should 
work with any fasta (my real data is not yet published, I can't share it 
publicly yet).
Tell me if you need more info
Anthony

On 11/06/2013 17:06, Carson Holt wrote:
> Could you send me your repeat_gff and genome fasta, so I can take a look.
>
> Thanks,
> Carson
>
>
>
> On 13-06-11 11:03 AM, "Anthony Bretaudeau"
> <anthony.bretaudeau at rennes.inra.fr> wrote:
>
>> Hello,
>> I have just tested with 2.28b: the problem is still there, and my fix
>> works on this version too.
>> Cheers
>> Anthony
>>
>> On 10/06/2013 18:13, Carson Holt wrote:
>>> Could you use MAKER version 2.28 instead (launch with maker -a if it
>>> still
>>> fails).
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 13-06-10 11:48 AM, "Anthony Bretaudeau"
>>> <anthony.bretaudeau at rennes.inra.fr> wrote:
>>>
>>>> Hello,
>>>> I am running Maker 2.27b on an insect genome, and I use a gff file
>>>> containing some repeat positions (rm_gff option in maker_opts.ctl).
>>>>
>>>> I encountered an error on 10 scaffolds (the genome contains ~40000
>>>> scaffolds) : "substr outside of string" (similar to this post:
>>>>
>>>> http://gmod.827538.n3.nabble.com/substr-outside-of-string-td4031889.html
>>>> ).
>>>>
>>>> After a lot a debugging, it turns out the problem came from the code of
>>>> "phathits_on_chunk" function in lib/GFFDB.pm, near line 539: there is a
>>>> SQL query that fetches features that overlap with the border of the
>>>> sequence chunk.
>>>> The problem is that it also fetches features that are completely
>>>> outside
>>>> of the chunk in the same region. This produces an error when maker
>>>> tries
>>>> to mask the sequence as it does a substr outside the string.
>>>>
>>>> I fixed it by patching lib/repeat_mask_seq.pm, near line 138:
>>>> I replaced:
>>>>             substr($$seq, $b -1 , $l, "$replace"x$l);
>>>> By:
>>>>         if ($b < length($$seq)) {
>>>>             substr($$seq, $b -1 , $l, "$replace"x$l);
>>>>         }
>>>>
>>>> I don't know if there is a more elegant solution, but this seems to
>>>> solve the problem.
>>>>
>>>> Cheers
>>>> Anthony
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

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